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Liu Y, Wang Y, Willett SD, Zimmermann NE, Pellissier L. Escarpment evolution drives the diversification of the Madagascar flora. Science 2024; 383:653-658. [PMID: 38330102 DOI: 10.1126/science.adi0833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024]
Abstract
Madagascar exhibits high endemic biodiversity that has evolved with sustained and stable rates of speciation over the past several tens of millions of years. The topography of Madagascar is dominated by a mountainous continental rift escarpment, with the highest plant diversity and rarity found along the steep, eastern side of this geographic feature. Using a process-explicit model, we show that precipitation-driven erosion and landward retreat of this high-relief topography creates transient habitat organization through multiple mechanisms, including catchment expansion, isolation of highland remnants, and formation of topographic barriers. Habitat isolation and reconnection on a million-year timescale serves as an allopatric speciation pump creating the observed biodiversity.
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Affiliation(s)
- Yi Liu
- Swiss Federal Research Institute (WSL), 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Yanyan Wang
- Department of Earth Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Sean D Willett
- Department of Earth Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Niklaus E Zimmermann
- Swiss Federal Research Institute (WSL), 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Loïc Pellissier
- Swiss Federal Research Institute (WSL), 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
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Guo WY, Serra-Diaz JM, Eiserhardt WL, Maitner BS, Merow C, Violle C, Pound MJ, Sun M, Slik F, Blach-Overgaard A, Enquist BJ, Svenning JC. Climate change and land use threaten global hotspots of phylogenetic endemism for trees. Nat Commun 2023; 14:6950. [PMID: 37907453 PMCID: PMC10618213 DOI: 10.1038/s41467-023-42671-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
Across the globe, tree species are under high anthropogenic pressure. Risks of extinction are notably more severe for species with restricted ranges and distinct evolutionary histories. Here, we use a global dataset covering 41,835 species (65.1% of known tree species) to assess the spatial pattern of tree species' phylogenetic endemism, its macroecological drivers, and how future pressures may affect the conservation status of the identified hotspots. We found that low-to-mid latitudes host most endemism hotspots, with current climate being the strongest driver, and climatic stability across thousands to millions of years back in time as a major co-determinant. These hotspots are mostly located outside of protected areas and face relatively high land-use change and future climate change pressure. Our study highlights the risk from climate change for tree diversity and the necessity to strengthen conservation and restoration actions in global hotspots of phylogenetic endemism for trees to avoid major future losses of tree diversity.
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Affiliation(s)
- Wen-Yong Guo
- Research Center for Global Change and Complex Ecosystems & Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, 200241, Shanghai, P. R. China.
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, 8000, Aarhus C, Denmark.
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark.
| | - Josep M Serra-Diaz
- Eversource Energy Center and Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Université de Lorraine, AgroParisTech, INRAE, Silva, Nancy, France
| | - Wolf L Eiserhardt
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
| | - Brian S Maitner
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Cory Merow
- Eversource Energy Center and Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Matthew J Pound
- Department of Geography and Environmental Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Miao Sun
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Ferry Slik
- Environmental and Life Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, BE1410, Gadong, Brunei Darussalam
| | - Anne Blach-Overgaard
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
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González-Orozco CE. Unveiling evolutionary cradles and museums of flowering plants in a neotropical biodiversity hotspot. R Soc Open Sci 2023; 10:230917. [PMID: 37830028 PMCID: PMC10565361 DOI: 10.1098/rsos.230917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023]
Abstract
Colombia, renowned as an important centre of global biodiversity, continues to harbour undiscovered evolutionary hotspots of flowering plants. The altitude-dependent hypothesis suggests that richness patterns are determined by altitude and probably influenced by climate variables. This study employs null models based on a species-level phylogeny of Colombia's flowering plants and their geographical distributions to identify evolutionary hotspots. We explore the potential correlation between elevation, climate variables such as temperature and rainfall, and the location and nature of these hotspots. The findings reveal that evolutionary cradles, which house young endemic species, are predominantly located in the mountainous regions of the Andes. Conversely, evolutionary museums, hosting older endemic species, are found in lowland regions spanning the Caribbean, Orinoco, Amazon and Pacific areas. These results demonstrate a clear elevational segregation of evolutionary hotspots, primarily influenced by temperature, thereby supporting the hypothesis under examination. Furthermore, this study identifies previously unrecognized evolutionary regions, highlighting the limited understanding of Colombia's biodiversity distribution and evolutionary history.
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Affiliation(s)
- Carlos E. González-Orozco
- Corporación Colombiana de Investigación Agropecuaria- Agrosavia, Centro de Investigación La Libertad- Km 14 vía Villavicencio-Puerto López, Meta, Colombia
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Calvente A, da Silva APA, Edler D, Carvalho FA, Fantinati MR, Zizka A, Antonelli A. Spiny but photogenic: Amateur sightings complement herbarium specimens to reveal the bioregions of cacti. Am J Bot 2023; 110:e16235. [PMID: 37661935 DOI: 10.1002/ajb2.16235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/05/2023]
Abstract
PREMISE Cacti are characteristic elements of the Neotropical flora and of major interest for biogeographic, evolutionary, and ecological studies. We tested global biogeographic boundaries for Neotropical Cactaceae using specimen-based occurrences, coupled with data from visual observations, as a means to tackle the known collection biases in the family. METHODS Species richness and record density were assessed for preserved specimens and human observations, and a bioregional scheme tailored to Cactaceae was produced using the interactive web application Infomap Bioregions, based on data from 261,272 point records cleaned through automated and manual steps. RESULTS We found that areas in Mexico and southwestern USA, in eastern Brazil, and along the Andean region have the greatest density of records and the highest species richness. Human observations complement information from preserved specimens substantially, especially along the Andes. We propose 24 cactus bioregions, among which the most species-rich are northern Mexico/southwestern USA, central Mexico, southern central Mexico, Central America, Mexican Pacific coast, central and southern Andes, northwestern Mexico/extreme southwestern USA, southwestern Bolivia, northeastern Brazil, and Mexico/Baja California. CONCLUSIONS The bioregionalization proposed shows biogeographic boundaries specific to cacti and can thereby aid further evolutionary, biogeographic, and ecological studies by providing a validated framework for further analyses. This classification builds upon, and is distinctive from, other expert-derived regionalization schemes for other taxa. Our results showcase how observation data, including citizen-science records, can complement traditional specimen-based data for biogeographic research, particularly for taxa with specific specimen collection and preservation challenges and those that are threatened or internationally protected.
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Affiliation(s)
- Alice Calvente
- Laboratório de Botânica Sistemática, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, 3000, CEP 59078970, Lagoa Nova, Natal, RN, Brazil
| | - Ana Paula Alves da Silva
- Laboratório de Botânica Sistemática, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, 3000, CEP 59078970, Lagoa Nova, Natal, RN, Brazil
| | - Daniel Edler
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Fernanda Antunes Carvalho
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Pampulha, CEP 31270-901, Belo Horizonte, MG, Brazil
| | - Mariana Ramos Fantinati
- Departamento de Ciências Biológicas, Universidade Estadual Paulista-câmpus de Assis, Av. Dom Antônio, 2100, Parque Universitário, CEP 19806-900, Assis, SP, Brazil
| | - Alexander Zizka
- Biodiversity of plants, Philipps University Marburg, Marburg, 35043, Germany
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30, Gothenburg, Sweden
- Royal Botanic Gardens Kew, TW9 3AE, Richmond, United Kingdom
- Department of Biology, University of Oxford, Oxford, OX1 3RB, United Kingdom
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Ramírez-Verdugo P, Tapia A, Forest F, Scherson RA. Evolutionary diversity of the endemic genera of the vascular flora of Chile and its implications for conservation. PLoS One 2023; 18:e0287957. [PMID: 37406022 DOI: 10.1371/journal.pone.0287957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
As a direct consequence of global change, both natural and human-induced, a high percentage of biodiversity is now under threat worldwide. This has urged conservation planners to formulate and/or improve existing strategies to preserve species and their ecosystems. In this context, the present study focuses on two strategies using phylogeny-based measures of biodiversity to account for the processes that led to the biodiversity patterns observed today. It will contribute additional information that can aid decision-making regarding the assignment of threat status for some species, thus strengthening measures currently in use and facilitate the allocation of often scarce conservation resources. The Evolutionarily Distinct (ED) index prioritises species that are on long branches of the tree of life with few descendants, and the Evolutionarily Distinct and Globally Endangered (EDGE) index integrates evolutionary history with IUCN Red List threat status of species. It has been used mostly in animal groups, but since the threats faced by many plants have not been evaluated, it has been more difficult to compile for plants worldwide. Here, we apply the EDGE metric to species of the endemic genera of Chile. However, more than 50% of the endemic flora of the country are still lacking official threat status. We thus used an alternative measure (Relative Evolutionary Distinctness-RED), based on a range-weighted phylogenetic tree, which uses geographic ranges to adjust branch lengths, and calculate ED. The RED index was shown to be a suitable measure, yielding similar results compared to EDGE, at least for this group of species. Given the urgency to halt biodiversity loss and the time it would take to evaluate all species, we propose that this index is used to set conservation priorities until we can calculate EDGE for these unique endemic species. This would allow guiding decision-making until we can gather more data to assess and assign conservation status to new species.
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Affiliation(s)
- Pamela Ramírez-Verdugo
- Herbario VALPL y Laboratorio de Botánica, Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso, Chile
- Jardín Botánico Nacional, Viña del Mar, Chile
- Laboratorio de Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Alexis Tapia
- Departamento de Matemática, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Rosa A Scherson
- Laboratorio de Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
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Gutiérrez-Rodríguez BE, Vásquez-Cruz M, Sosa V. Phylogenetic endemism of the orchids of Megamexico reveals complementary areas for conservation. Plant Divers 2022; 44:351-359. [PMID: 35967260 PMCID: PMC9363653 DOI: 10.1016/j.pld.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 06/15/2023]
Abstract
Orchid diversity provides a unique opportunity to further our understanding of biotic and abiotic factors linked to patterns of richness, endemism, and phylogenetic endemism in many regions. However, orchid diversity is consistently threatened by illegal trade and habitat transformation. Here, we identified areas critical for orchid conservation in the biogeographic province of Megamexico. For this purpose, we evaluated orchid endemism, phylogenetic diversity, and phylogenetic endemism within Megamexico and characterized orchid life forms. Our results indicate that the majority of the regions with the highest estimates of endemism and phylogenetic endemism are in southern Mexico and northern Central America, mostly located on the Pacific side of Megamexico. Among the most important orchid lineages, several belong to epiphytic lineages such as Pleurothallidinae, Laeliinae and Oncidiinae. We also found that species from diverse and distantly related lineages converge in montane forests where suitable substrates for epiphytes abound. Furthermore, the southernmost areas of phylogenetic diversity and endemism of Megamexico are in unprotected areas. Thus, we conclude that the most critical areas for orchid conservation in Megamexico are located in southern Mexico and northern Central America. We recommend that these areas should be given priority by the Mexican system of natural protected areas as complementary conservation areas.
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Affiliation(s)
| | - Marilyn Vásquez-Cruz
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para La Biodiversidad, Centro de Investigación y Estudios Avanzados Irapuato, Libramiento Norte Carretera León Km. 9.6, 36821 Irapuato, Guanajuato, Mexico
| | - Victoria Sosa
- Instituto de Ecología AC, Carretera Antigua a Coatepec 351, El Haya, 91073 Xalapa, Veracruz, Mexico
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Nitta JH, Mishler BD, Iwasaki W, Ebihara A. Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation. Am J Bot 2022; 109:727-745. [PMID: 35435239 PMCID: PMC9325522 DOI: 10.1002/ajb2.1848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 06/02/2023]
Abstract
PREMISE Biodiversity is often only measured with species richness; however, this metric ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan. METHODS We compiled a community data set of 1239 grid cells (20 × 20 km each) including 672 taxa based on >300,000 specimen records. We combined the community data with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid cells with conservation zones and range maps of native Japanese deer. RESULTS Taxonomic richness was highest at mid-latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid-latitudes. Grid cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics. CONCLUSIONS Our integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple metrics when establishing conservation priorities.
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Affiliation(s)
- Joel H. Nitta
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Brent D. Mishler
- University and Jepson Herbaria, and Department of Integrative BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
- Department of Integrated Biosciences, Graduate School of Frontier SciencesThe University of TokyoChibaJapan
| | - Atsushi Ebihara
- Department of BotanyNational Museum of Nature and ScienceTsukubaJapan
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Silva DC, Oliveira HFM, Zangrandi PL, Domingos FMCB. Flying Over Amazonian Waters: The Role of Rivers on the Distribution and Endemism Patterns of Neotropical Bats. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.774083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Amazon comprises many of the largest rivers in the planet and also houses some of the richest bat communities in the world. Rivers are important geographic barriers for the dispersal and distribution of different taxa worldwide and, particularly in the Amazon region, they form the conceptual and empirical bases for the recognition of the so-called Areas of Endemism of terrestrial vertebrates. Despite the vast literature on the role of rivers on vertebrate community structure in the Amazon Forest, this process has never been investigated using a comprehensive dataset of Neotropical bat communities in the region. In this study, we aimed at: (1) evaluating the patterns of bat endemism across the Amazon Forest; (2) testing for the relationship between the distribution of bat species in the Amazon and the interfluve Areas of Endemism as currently recognized, and; (3) analyzing the importance of major Amazonian rivers in bat beta-diversity (turnover and nestedness) in the Amazon. Our results indicate that rivers are not major barriers for the current distribution of most bat species, and bat community composition breaks were divided into two clusters separating the east and west regions, and a third cluster in northern Amazon. In addition, there was no significant overlap among species distribution limits and the interfluve Areas of Endemism. Interestingly, the geographic patterns that we found for bat communities composition breaks highly resembles the one recovered using bird communities, suggesting that similar ecological and historical drivers might be acting to determine the distribution of flying vertebrates in the Amazon. Moreover, Amazonian bat distribution and endemism patterns were likely shaped by factors other than rivers, such as species interactions and the current environmental conditions. In conclusion, our results highlight the importance of modern analytical approaches to investigate large scale ecological patterns in the Neotropical region, and also challenge the widely recognized role of rivers on the determination of community structure and endemism patterns in the Amazon Forest, at least for bats.
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Andermann T, Antonelli A, Barrett RL, Silvestro D. Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning. Front Plant Sci 2022; 13:839407. [PMID: 35519811 PMCID: PMC9062518 DOI: 10.3389/fpls.2022.839407] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
The reliable mapping of species richness is a crucial step for the identification of areas of high conservation priority, alongside other value and threat considerations. This is commonly done by overlapping range maps of individual species, which requires dense availability of occurrence data or relies on assumptions about the presence of species in unsampled areas deemed suitable by environmental niche models. Here, we present a deep learning approach that directly estimates species richness, skipping the step of estimating individual species ranges. We train a neural network model based on species lists from inventory plots, which provide ground truth data for supervised machine learning. The model learns to predict species richness based on spatially associated variables, including climatic and geographic predictors, as well as counts of available species records from online databases. We assess the empirical utility of our approach by producing independently verifiable maps of alpha, beta, and gamma plant diversity at high spatial resolutions for Australia, a continent with highly heterogeneous diversity patterns. Our deep learning framework provides a powerful and flexible new approach for estimating biodiversity patterns, constituting a step forward toward automated biodiversity assessments.
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Affiliation(s)
- Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Russell L. Barrett
- Royal Botanic Gardens, Sydney, NSW, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
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10
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Zhang XX, Ye JF, Laffan SW, Mishler BD, Thornhill AH, Lu LM, Mao LF, Liu B, Chen YH, Lu AM, Miller JT, Chen ZD. Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation. J Integr Plant Biol 2022; 64:105-117. [PMID: 34773376 DOI: 10.1111/jipb.13189] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/16/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies. However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China. We conducted a spatial phylogenetic analysis of the Chinese angiosperm flora at the generic level to identify centers of neo- and paleo-endemism. Our results indicate that: (i) the majority of grid cells in China with significantly high phylogenetic endemism (PE) were located in the mountainous regions; (ii) four of the nine centers of endemism recognized, located in northern and western China, were recognized for the first time; (iii) arid and semiarid regions in Northwest China were commonly linked to significant PE, consistent with other spatial phylogenetic studies worldwide; and (iv) six high-priority conservation gaps were detected by overlaying the boundaries of China's nature reserves on all significant PE cells. Overall, we conclude that the mountains of southern and northern China contain both paleo-endemics (ancient relictual lineages) and neo-endemics (recently diverged lineages). The areas we highlight as conservation priorities are important for broad-scale planning, especially in the context of evolutionary history preservation.
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Affiliation(s)
- Xiao-Xia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jian-Fei Ye
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Shawn W Laffan
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Brent D Mishler
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | - Andrew H Thornhill
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
- The University of Adelaide, Environment Institute, Adelaide, SA, 5005, Australia
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Department for Environment and Water, Adelaide, SA, 5001, Australia
| | - Li-Min Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Ling-Feng Mao
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Sino-Africa Joint Research Center, the Chinese Academy of Sciences, Wuhan, 430074, China
| | - You-Hua Chen
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, 610041, China
| | - An-Ming Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Joseph T Miller
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Department for Environment and Water, Adelaide, SA, 5001, Australia
- Global Biodiversity Information Facility, Copenhagen, Denmark
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Sino-Africa Joint Research Center, the Chinese Academy of Sciences, Wuhan, 430074, China
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González‐Orozco CE, Sosa CC, Thornhill AH, Laffan SW. Phylogenetic diversity and conservation of crop wild relatives in Colombia. Evol Appl 2021; 14:2603-2617. [PMID: 34815742 PMCID: PMC8591330 DOI: 10.1111/eva.13295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/29/2022] Open
Abstract
Crop wild relatives (CWR) are an important agricultural resource as they contain genetic traits not found in cultivated species due to localized adaptation to unique environmental and climatic conditions. Phylogenetic diversity (PD) measures the evolutionary relationship of species using the tree of life. Our knowledge of CWR PD in neotropical regions is in its infancy. We analysed the distribution of CWR PD across Colombia and assessed its conservation status. The areas with the largest concentration of PD were identified as being in the northern part of the central and western Andean mountain ranges and the Pacific region. These centres of high PD were comprised of predominantly short and closely related branches, mostly of species of wild tomatoes and black peppers. In contrast, the CWR PD in the lowland ecosystems of the Amazon and Orinoquia regions had deeply diverging clades predominantly represented by long and distantly related branches (i.e. tuberous roots, grains and cacao). We categorized 50 (52.6%) of the CWR species as 'high priority', 36 as 'medium priority' and nine as 'low priority' for further ex-situ and in situ conservation actions. New areas of high PD and richness with large ex-situ gap collections were identified mainly in the northern part of the Andes of Colombia. We found that 56% of the grid cells with the highest PD values were unprotected. These baseline data could be used to create a comprehensive national strategy of CWR conservation in Colombia.
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Affiliation(s)
- Carlos E. González‐Orozco
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)Centro de Investigación La LibertadVillavicencioColombia
| | - Chrystian C. Sosa
- Departamento de Ciencias naturales y MatemáticasPontificia Universidad Javeriana CaliCaliColombia
- Grupo de Investigación en EvoluciónEcología y Conservación EECOPrograma de BiologíaFacultad de Ciencias Básicas y TecnologíasUniversidad del QuindíoArmeniaColombia
| | - Andrew H. Thornhill
- Environment InstituteThe University of AdelaideAdelaideSAAustralia
- Department for Environment and WaterState Herbarium of South AustraliaBotanic Gardens and State HerbariumAdelaideSAAustralia
| | - Shawn W. Laffan
- Earth and Sustainability Science Research CentreSchool of Biological, Earth and Environmental SciencesThe University of New South WalesKensingtonNSWAustralia
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12
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Acevedo S, Sandel B. Phylogenetic Endemism Hotspots of North American Birds Are Associated With Warm Temperatures and Long- and Short-Term Climate Stability. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.645396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human activities have dramatically altered the distribution and abundance of species, and our impacts are likely to increase in the near future. Conservation efforts are typically faced with scarce resources, forcing us to prioritize areas based in part on estimates of their conservation value. Two major factors in conservation value are a species uniqueness and its extinction risk. Though these ideas are multidimensional, one important component of uniqueness is evolutionary distinctness, while risk is strongly related to geographic range size. These components are combined in an assemblage-level measure called phylogenetic endemism (PE), which measures the degree to which the species in an assemblage are small-ranged and phylogenetically distinct. Broad-scale patterns and correlates of PE are becoming better known for a variety of groups, and have been shown to depend on current climate, geographic isolation and long-term climate stability. Human impacts (e.g., land cover changes), are likely to shape PE as well, though the coarse resolution of most previous studies may make this difficult to detect. Overall, PE patterns at fine spatial and temporal resolutions are not well understood. Here, we fill this gap using data from the North American Breeding Bird Survey. These data comprise a long-term annual record with fine spatial resolution and a near-continental extent. We assess geographic patterns and trends in PE, and relate these to a range of putative predictor variables including measures of current climate, land cover, long-term and recent climate change. Bird PE is concentrated in three main hotspots: the west coast, the southeast and south-central Canada east of the Rockies. High PE values tended to occur in regions with high temperatures and stability in temperature, both in the long (21,000 year) and short (35 year) time scales. PE patterns are driven more strongly by patterns of range size than phylogenetic distinctiveness, and are trending gradually upward, driven by increasingly frequent sightings of small-ranged species. These results indicate the importance of climate stability on multiple time scales in influencing endemism patterns and suggest a surprisingly minor influence of direct human land use. The increase in PE through time may reflect successful conservation efforts that have led to population recoveries of some small-ranged species.
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Flores-Tolentino M, Beltrán-Rodríguez L, Morales-Linares J, Ramírez Rodríguez JR, Ibarra-Manríquez G, Dorado Ó, Villaseñor JL. Biogeographic regionalization by spatial and environmental components: Numerical proposal. PLoS One 2021; 16:e0253152. [PMID: 34129612 PMCID: PMC8205180 DOI: 10.1371/journal.pone.0253152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/29/2021] [Indexed: 11/19/2022] Open
Abstract
Regionalization through the analysis of species groups offers important advantages in conservation biology, compared to the single taxon approach in areas of high species richness. We use a systematic framework for biogeographic regionalization at a regional scale based on species turnover and environmental drivers (climate variables and soil properties) mainly of herbaceous plant species richness. To identify phytogeographic regions in the Balsas Depression (BD), we use Asteraceae species, a family widely distributed in Seasonally Dry Tropical Forest (SDTF) and the most diverse of the vascular plants in Mexico. Occurrence records of 571 species were used to apply a quantitative analysis based on the species turnover, the rate of changes in their composition between sites (β-Simpson index) and the analysis of the identified environmental drivers. Also, the environmental predictors that influence species richness in the SDTF were determined with a redundancy analysis. We identified and named two phytogeographic districts within the SDTF of the BD (Upper Balsas and Lower Balsas). According to the multi-response permutation procedure, floristic composition of the two districts differs significantly, and the richness of exclusive species in Upper Balsas was higher (292 species) than in the Lower Balsas (32 species). The proportion of Mg and Ca in the soil and the precipitation of the driest three-month period were the environmental factors with greatest positive influence on species richness. The division of geographic districts subordinated to the province level, based on diverse families such as Asteraceae, proved to be appropriate to set up strategies for the conservation of the regional flora, since at this scale, variation in species richness is more evident. Our findings are consistent with a growing body of biogeographic literature that indicates that the identification of smaller biotic districts is more efficient for the conservation of biodiversity, particularly of endemic or rare plants, whose distribution responds more to microhabitats variation.
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Affiliation(s)
- Mayra Flores-Tolentino
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Leonardo Beltrán-Rodríguez
- Jardín Botánico–Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico
| | - Jonas Morales-Linares
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - J. Rolando Ramírez Rodríguez
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Guillermo Ibarra-Manríquez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
| | - Óscar Dorado
- Centro de Educación Ambiental e Investigación Sierra de Huautla, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - José Luis Villaseñor
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Cheikh Albassatneh M, Escudero M, Monnet A, Arroyo J, Bacchetta G, Bagnoli F, Dimopoulos P, Hampe A, Leriche A, Médail F, Nikolic T, Ponger L, Vendramin GG, Fady B. Spatial patterns of genus‐level phylogenetic endemism in the tree flora of Mediterranean Europe. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Marwan Cheikh Albassatneh
- Institut de Systématique, Evolution, Biodiversité (ISYEB) Muséum national d’Histoire naturelle (MNHN), CNRS, Sorbonne Université, EPHE, Université des Antilles Paris France
- Aix Marseille Université, Avignon Université, CNRS, IRD IMBE Aix‐en‐Provence France
- Institute of Ecology and Environmental Sciences Sorbonne University Paris France
| | - Marcial Escudero
- Department of Plant Biology and Ecology University of Seville Seville Spain
| | - Anne‐Christine Monnet
- Institut de Systématique, Evolution, Biodiversité (ISYEB) Muséum national d’Histoire naturelle (MNHN), CNRS, Sorbonne Université, EPHE, Université des Antilles Paris France
- Aix Marseille Université, Avignon Université, CNRS, IRD IMBE Aix‐en‐Provence France
| | - Juan Arroyo
- Department of Plant Biology and Ecology University of Seville Seville Spain
| | - Gianluigi Bacchetta
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | | | | | - Arndt Hampe
- BIOGECO INRAE, Bordeaux University Cestas France
| | - Agathe Leriche
- Aix Marseille Université, Avignon Université, CNRS, IRD IMBE Aix‐en‐Provence France
| | - Frédéric Médail
- Aix Marseille Université, Avignon Université, CNRS, IRD IMBE Aix‐en‐Provence France
| | - Toni Nikolic
- Department of Botany Faculty of Science University of Zagreb Zagreb Croatia
| | - Loïc Ponger
- Structure et Instabilité des Génomes "Muséum National d'Histoire Naturelle" (MNHN), CNRS Paris France
| | | | - Bruno Fady
- Ecology of Mediterranean Forests (URFM) INRAE Avignon France
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15
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Zhu Z, Harris AJ, Nizamani MM, Thornhill AH, Scherson RA, Wang H. Spatial phylogenetics of the native woody plant species in Hainan, China. Ecol Evol 2021; 11:2100-2109. [PMID: 33717445 PMCID: PMC7920777 DOI: 10.1002/ece3.7180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/05/2020] [Accepted: 12/18/2020] [Indexed: 11/08/2022] Open
Abstract
To better identify biodiversity hotspots for conservation on Hainan Island, a tropical island in southern China, we assessed spatial variation in phylogenetic diversity and species richness using 18,976 georeferenced specimen records and a newly reconstructed molecular phylogeny of 957 native woody plants. Within this framework, we delineated bioregions based on vegetation composition and mapped areas of neoendemism and paleoendemism to identify areas of priority for conservation. Our results reveal that the southwest of Hainan is the most important hot spot for endemism and plant diversity followed by the southeast area. The distribution of endemic species showed a scattered, rather than clustered, pattern on the island. Based on phylogenetic range-weighted turnover metrics, we delineated three major vegetational zones in Hainan. These largely correspond to natural secondary growth and managed forests (e.g., rubber and timber forests) in central Hainan, old-growth forests and natural secondary growth forest at the margins of Hainan, and nature reserves on the island (e.g., Jianfeng and Diaoluo National Nature Reserves). Our study helps to elucidate potential botanical conservation priorities for Hainan within an evolutionary, phylogenetic framework.
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Affiliation(s)
- Zhi‐Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of ScienceGuangzhouChina
| | - Mir Muhammad Nizamani
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Andrew H. Thornhill
- Department for Environment and WaterState Herbarium of South AustraliaBotanic Gardens and State HerbariumAdelaideSAAustralia
| | - Rosa A. Scherson
- Departamento de Silvicultura y Conservación de la NaturalezaFacultad de Ciencias Forestales y Conservación de la NaturalezaUniversidad de ChileSantiagoChile
| | - Hua‐Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
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16
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Kougioumoutzis K, Kokkoris IP, Panitsa M, Kallimanis A, Strid A, Dimopoulos P. Plant Endemism Centres and Biodiversity Hotspots in Greece. Biology (Basel) 2021; 10:72. [PMID: 33498512 PMCID: PMC7909545 DOI: 10.3390/biology10020072] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/11/2021] [Accepted: 01/17/2021] [Indexed: 12/21/2022]
Abstract
Biodiversity hotspots (BH) cover a small fraction of the Earth's surface, yet host numerous endemics. Human-induced biodiversity loss has been increasing worldwide, despite attempts to halt the extinction crisis. There is thus an urgent need to efficiently allocate the available conservation funds in an optimised conservation prioritization scheme. Identifying BH and endemism centres (EC) is therefore a valuable tool in conservation prioritization and planning. Even though Greece is one of the most plant species-rich European countries, few studies have dealt with the identification of BH or EC and none has ever incorporated phylogenetic information or extended to the national scale. Consequently, we are unaware of the extent that Special Areas of Conservation (SAC) of the Natura 2000 network efficiently protect Greek plant diversity. Here, we located for the first time at a national scale and in a phylogenetic framework, the areas serving as BH and EC, and assessed the effectiveness of the Greek SAC in safeguarding them. BH and EC are mainly located near mountainous areas, and in areas supposedly floristically impoverished, such as the central Aegean islands. A critical re-assessment of the Greek SAC might be needed to minimize the extinction risk of the Greek endemics, by focusing the conservation efforts also on the BH and EC that fall outside the established Greek SAC.
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Affiliation(s)
- Konstantinos Kougioumoutzis
- Division of Plant Biology, Laboratory of Botany, Department of Biology, University of Patras, 26504 Patras, Greece; (I.P.K.); (M.P.); (P.D.)
- Department of Ecology and Systematics, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Ioannis P. Kokkoris
- Division of Plant Biology, Laboratory of Botany, Department of Biology, University of Patras, 26504 Patras, Greece; (I.P.K.); (M.P.); (P.D.)
| | - Maria Panitsa
- Division of Plant Biology, Laboratory of Botany, Department of Biology, University of Patras, 26504 Patras, Greece; (I.P.K.); (M.P.); (P.D.)
| | - Athanasios Kallimanis
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | | | - Panayotis Dimopoulos
- Division of Plant Biology, Laboratory of Botany, Department of Biology, University of Patras, 26504 Patras, Greece; (I.P.K.); (M.P.); (P.D.)
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Affiliation(s)
- Barnabas H. Daru
- Department of Life Sciences Texas A&M University‐Corpus Christi, Corpus Christi TX USA
| | - Piyal Karunarathne
- Department of Life Sciences Texas A&M University‐Corpus Christi, Corpus Christi TX USA
| | - Klaus Schliep
- Institute of Computational Biotechnology Graz University of Technology Graz Styria Austria
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18
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Kougioumoutzis K, Kokkoris IP, Panitsa M, Trigas P, Strid A, Dimopoulos P. Spatial Phylogenetics, Biogeographical Patterns and Conservation Implications of the Endemic Flora of Crete (Aegean, Greece) under Climate Change Scenarios. Biology (Basel) 2020; 9:E199. [PMID: 32751787 DOI: 10.3390/biology9080199] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022]
Abstract
Human-induced biodiversity loss has been accelerating since the industrial revolution. The climate change impacts will severely alter the biodiversity and biogeographical patterns at all scales, leading to biotic homogenization. Due to underfunding, a climate smart, conservation-prioritization scheme is needed to optimize species protection. Spatial phylogenetics enable the identification of endemism centers and provide valuable insights regarding the eco-evolutionary and conservation value, as well as the biogeographical origin of a given area. Many studies exist regarding the conservation prioritization of mainland areas, yet none has assessed how climate change might alter the biodiversity and biogeographical patterns of an island biodiversity hotspot. Thus, we conducted a phylogenetically informed, conservation prioritization study dealing with the effects of climate change on Crete’s plant diversity and biogeographical patterns. Using several macroecological analyses, we identified the current and future endemism centers and assessed the impact of climate change on the biogeographical patterns in Crete. The highlands of Cretan mountains have served as both diversity cradles and museums, due to their stable climate and high topographical heterogeneity, providing important ecosystem services. Historical processes seem to have driven diversification and endemic species distribution in Crete. Due to the changing climate and the subsequent biotic homogenization, Crete’s unique bioregionalization, which strongly reminiscent the spatial configuration of the Pliocene/Pleistocene Cretan paleo-islands, will drastically change. The emergence of the ‘Anthropocene’ era calls for the prioritization of biodiversity-rich areas, serving as mixed-endemism centers, with high overlaps among protected areas and climatic refugia.
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Murphy DJ, Ebach MC, Miller JT, Laffan SW, Cassis G, Ung V, Thornhill AH, Kerr N, Tursky ML. Do phytogeographic patterns reveal biomes or biotic regions? Cladistics 2019; 35:654-670. [DOI: 10.1111/cla.12381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - Malte C. Ebach
- Palaeontology, Geobiology and Earth Archives Research Centre (PANGEA) School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW 2052 Australia
| | - Joseph T. Miller
- Office of International Science and Engineering National Science Foundation Arlington VA 22230 USA
| | - Shawn W. Laffan
- School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW 2052 Australia
| | - Gerasimos Cassis
- School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW 2052 Australia
| | - Visotheary Ung
- Institut de Systématique Evolution, Biodiversité (ISYEB) Muséum National d'Histoire naturelle CNRS Sorbonne Université EPHE UA, CP 50, 45 rue Buffon 75005 Paris France
| | - Andrew H. Thornhill
- Australian Tropical Herbarium James Cook University Cairns Qld 4870 Australia
| | - Nunzio Kerr
- Centre for Australian National Biodiversity Research CSIRO National Research Collections Australia PO Box 1700 Canberra ACT 2601 Australia
| | - Melinda L. Tursky
- Department of Haematology and BM Transplant St Vincent's Hospital Sydney NSW 2010 Australia
- Blood, Stem Cell and Cancer Research Programme St Vincent's Centre for Applied Medical Research Sydney NSW 2010 Australia
- Faculty of Medicine St Vincent's Clinical School University of New South Wales Sydney NSW 2052 Australia
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20
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Cantrill DJ. The Australasian Virtual Herbarium: Tracking data usage and benefits for biological collections. Appl Plant Sci 2018; 6:e1026. [PMID: 29732257 PMCID: PMC5851564 DOI: 10.1002/aps3.1026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/30/2018] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Globally, natural history collections are focused on digitizing specimens and information and making these data accessible. Usage information on National Herbarium of Victoria data made available through the Atlas of Living Australia and The Australasian Virtual Herbarium (AVH) is analyzed to understand how and by whom herbarium data are being used. METHODS Since 2010, AVH data usage information has been gathered from users and supplied to data custodians as a spreadsheet that includes number of download events, number of records downloaded, and user reasons for downloading data in predefined categories. RESULTS Since 2010, in excess of 268,000 download events of 194 million records (excluding testing events) have been recorded for the National Herbarium of Victoria data set. This means, on average, every record has been downloaded 220 times in the past nine years. Data use grew continuously from 2010 to 2015 but decreased in 2016 due to fewer ecological projects. DISCUSSION Data have primarily been used for ecological research, but there is an emerging trend for use in education including citizen science projects. Information about data use demonstrates relevance to funding agencies and helps inform the development of collections and prioritization of resources when digitizing material.
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Affiliation(s)
- David J. Cantrill
- Royal Botanic Gardens VictoriaPrivate Bag 2000, Birdwood AvenueSouth YarraVictoria3141Australia
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21
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Thornhill AH, Baldwin BG, Freyman WA, Nosratinia S, Kling MM, Morueta-Holme N, Madsen TP, Ackerly DD, Mishler BD. Spatial phylogenetics of the native California flora. BMC Biol 2017; 15:96. [PMID: 29073895 PMCID: PMC5658987 DOI: 10.1186/s12915-017-0435-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/05/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND California is a world floristic biodiversity hotspot where the terms neo- and paleo-endemism were first applied. Using spatial phylogenetics, it is now possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism, by combining spatial information from museum collections and DNA-based phylogenies. Here we used a distributional dataset of 1.39 million herbarium specimens, a phylogeny of 1083 operational taxonomic units (OTUs) and 9 genes, and a spatial randomization test to identify regions of significant phylogenetic diversity, relative phylogenetic diversity, and phylogenetic endemism (PE), as well as to conduct a categorical analysis of neo- and paleo-endemism (CANAPE). RESULTS We found (1) extensive phylogenetic clustering in the South Coast Ranges, southern Great Valley, and deserts of California; (2) significant concentrations of short branches in the Mojave and Great Basin Deserts and the South Coast Ranges and long branches in the northern Great Valley, Sierra Nevada foothills, and the northwestern and southwestern parts of the state; (3) significant concentrations of paleo-endemism in Northwestern California, the northern Great Valley, and western Sonoran Desert, and neo-endemism in the White-Inyo Range, northern Mojave Desert, and southern Channel Islands. Multiple analyses were run to observe the effects on significance patterns of using different phylogenetic tree topologies (uncalibrated trees versus time-calibrated ultrametric trees) and using different representations of OTU ranges (herbarium specimen locations versus species distribution models). CONCLUSIONS These analyses showed that examining the geographic distributions of branch lengths in a statistical framework adds a new dimension to California floristics that, in comparison with climatic data, helps to illuminate causes of endemism. In particular, the concentration of significant PE in more arid regions of California extends previous ideas about aridity as an evolutionary stimulus. The patterns seen are largely robust to phylogenetic uncertainty and time calibration but are sensitive to the use of occurrence data versus modeled ranges, indicating that special attention toward improving geographic distributional data should be top priority in the future for advancing understanding of spatial patterns of biodiversity.
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Affiliation(s)
- Andrew H Thornhill
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA.
| | - Bruce G Baldwin
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - William A Freyman
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Sonia Nosratinia
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Matthew M Kling
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Naia Morueta-Holme
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Thomas P Madsen
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - David D Ackerly
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Brent D Mishler
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
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Scherson RA, Thornhill AH, Urbina-Casanova R, Freyman WA, Pliscoff PA, Mishler BD. Spatial phylogenetics of the vascular flora of Chile. Mol Phylogenet Evol 2017; 112:88-95. [PMID: 28450227 DOI: 10.1016/j.ympev.2017.04.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/12/2017] [Accepted: 04/23/2017] [Indexed: 11/24/2022]
Abstract
Current geographic patterns of biodiversity are a consequence of the evolutionary history of the lineages that comprise them. This study was aimed at exploring how evolutionary features of the vascular flora of Chile are distributed across the landscape. Using a phylogeny at the genus level for 87% of the Chilean vascular flora, and a geographic database of sample localities, we calculated phylogenetic diversity (PD), phylogenetic endemism (PE), relative PD (RPD), and relative PE (RPE). Categorical Analyses of Neo- and Paleo-Endemism (CANAPE) were also performed, using a spatial randomization to assess statistical significance. A cluster analysis using range-weighted phylogenetic turnover was used to compare among grid cells, and with known Chilean bioclimates. PD patterns were concordant with known centers of high taxon richness and the Chilean biodiversity hotspot. In addition, several other interesting areas of concentration of evolutionary history were revealed as potential conservation targets. The south of the country shows areas of significantly high RPD and a concentration of paleo-endemism, and the north shows areas of significantly low PD and RPD, and a concentration of neo-endemism. Range-weighted phylogenetic turnover shows high congruence with the main macrobioclimates of Chile. Even though the study was done at the genus level, the outcome provides an accurate outline of phylogenetic patterns that can be filled in as more fine-scaled information becomes available.
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Edwards RD, Crisp MD, Cook DH, Cook LG. Congruent biogeographical disjunctions at a continent-wide scale: Quantifying and clarifying the role of biogeographic barriers in the Australian tropics. PLoS One 2017; 12:e0174812. [PMID: 28376094 PMCID: PMC5380322 DOI: 10.1371/journal.pone.0174812] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/15/2017] [Indexed: 11/18/2022] Open
Abstract
AIM To test whether novel and previously hypothesized biogeogaphic barriers in the Australian Tropics represent significant disjunction points or hard barriers, or both, to the distribution of plants. LOCATION Australian tropics: Australian Monsoon Tropics and Australian Wet Tropics. METHODS The presence or absence of 6,861 plant species was scored across 13 putative biogeographic barriers in the Australian Tropics, including two that have not previously been recognised. Randomizations of these data were used to test whether more species showed disjunctions (gaps in distribution) or likely barriers (range limits) at these points than expected by chance. RESULTS Two novel disjunctions in the Australian Tropics flora are identified in addition to eleven putative barriers previously recognized for animals. Of these, eleven disjunction points (all within the Australian Monsoon Tropics) were found to correspond to range-ending barriers to a significant number of species, while neither of the two disjunctions found within the Australian Wet Tropics limited a significant number of species' ranges. MAIN CONCLUSIONS Biogeographic barriers present significant distributional limits to native plant species in the Australian Monsoon Tropics but not in the Australian Wet Tropics.
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Affiliation(s)
- Robert D Edwards
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael D Crisp
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Dianne H Cook
- Department of Econometrics and Business Statistics, Monash University, Clayton, Victoria, Australia
| | - Lyn G Cook
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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Baldwin BG, Thornhill AH, Freyman WA, Ackerly DD, Kling MM, Morueta-Holme N, Mishler BD. Species richness and endemism in the native flora of California. Am J Bot 2017; 104:487-501. [PMID: 28341628 DOI: 10.3732/ajb.1600326] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/23/2017] [Indexed: 05/22/2023]
Abstract
PREMISE OF THE STUDY California's vascular flora is the most diverse and threatened in temperate North America. Previous studies of spatial patterns of Californian plant diversity have been limited by traditional metrics, non-uniform geographic units, and distributional data derived from floristic descriptions for only a subset of species. METHODS We revisited patterns of sampling intensity, species richness, and relative endemism in California based on equal-area spatial units, the full vascular flora, and specimen-based distributional data. We estimated richness, weighted endemism (inverse range-weighting of species), and corrected weighted endemism (weighted endemism corrected for richness), and performed a randomization test for significantly high endemism. KEY RESULTS Possible biases in herbarium data do not obscure patterns of high richness and endemism at the spatial resolution studied. High species richness was sometimes associated with significantly high endemism (e.g., Klamath Ranges) but often not. In Stebbins and Major's (1965) main endemism hotspot, Southwestern California, species richness is high across much of the Peninsular and Transverse ranges but significantly high endemism is mostly localized to the Santa Rosa and San Bernardino mountains. In contrast, species richness is low in the Channel Islands, where endemism is significantly high, as also found for much of the Death Valley region. CONCLUSIONS Measures of taxonomic richness, even with greater weighting of range-restricted taxa, are insufficient for identifying areas of significantly high endemism that warrant conservation attention. Differences between our findings and those in previous studies appear to mostly reflect the source and scale of distributional data, and recent analytical refinements.
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Affiliation(s)
- Bruce G Baldwin
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - Andrew H Thornhill
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - William A Freyman
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - David D Ackerly
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - Matthew M Kling
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - Naia Morueta-Holme
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - Brent D Mishler
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
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